I'm going on a mad RE-binge, and I'm also trying to piece every last part of the plot (that I can) together, Gaiden and Dead Aim and all.
First things first, the girl running around in RE4 is definitely the president's daughter - in the E3 demo, it says it's six years after the Raccoon City mayhem, Leon works for the feds now and is looking for the president's missing daughter. He then shows a photograph to some crazy spaniard that then tries to chop off his face, but er, it's the same girl in the screens, and unless Sherry was adopted or Billy Birkins' mutated and incinerated corpse was elected to office, it's definitely not Sherry.
I have some theories about who is behind what in RE4, and I think we should have a storyline thread.